Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes

Abstract

Nucleo-cytoplasmic large DNA viruses (NCLDVs) constitute a group of eukaryotic viruses that can have crucial ecological roles in the sea by accelerating the turnover of their unicellular hosts or by causing diseases in animals. To better characterize the diversity, abundance and biogeography of marine NCLDVs, we analyzed 17 metagenomes derived from microbial samples (0.2–1.6 μm size range) collected during the Tara Oceans Expedition. The sample set includes ecosystems under-represented in previous studies, such as the Arabian Sea oxygen minimum zone (OMZ) and Indian Ocean lagoons. By combining computationally derived relative abundance and direct prokaryote cell counts, the abundance of NCLDVs was found to be in the order of 104–105 genomes ml−1 for the samples from the photic zone and 102–103 genomes ml−1 for the OMZ. The Megaviridae and Phycodnaviridae dominated the NCLDV populations in the metagenomes, although most of the reads classified in these families showed large divergence from known viral genomes. Our taxon co-occurrence analysis revealed a potential association between viruses of the Megaviridae family and eukaryotes related to oomycetes. In support of this predicted association, we identified six cases of lateral gene transfer between Megaviridae and oomycetes. Our results suggest that marine NCLDVs probably outnumber eukaryotic organisms in the photic layer (per given water mass) and that metagenomic sequence analyses promise to shed new light on the biodiversity of marine viruses and their interactions with potential hosts.

Host-derived viral transporter protein for nitrogen uptake in infected marine phytoplankton

“…This intermediate phylogenetic position was also found in a ML phylogenetic tree of the viral DNA polymerase B (915 sites; SI Appendix, Fig. S2) a gene commonly used as a marker for NCLDV phylogenetic and diversity analyses (48)(49)(50).…”

“…To investigate the wider distribution of vAmt-like homologs, we screened metagenomes for similar sequences in the Global Ocean Sampling and Tara Oceans giant virus datasets (50) as well as all aquatic metagenomes available at iMicrobe (94). Putative vAmt homologs were aligned to alignment corresponding to the vAmt subtree ( Fig.…”

High Throughput Sequencing: An Overview of Sequencing Chemistry

“…The isolated DNA is fragmented in the range from 150 to 800 bp depending on the platform to be used and is done by one of the three following methods i.e. physical/mechanical methods (i.e., Nebulization and ultrasonication) or enzymatic methods (i.e., non-specific endonuclease cocktails) and transposase (tagmentation reactions) [10][11][12][13]. Library preparation from RNA is done by capturing mRNA, random priming and complementary DNA (cDNA) synthesis followed by the end polishing and adapter ligation [14][15][16].…”

Systems ecology: Biology on the high seas

“…Seeing which organisms occur alongside others in samples, for example, can suggest possible interactions. Hiroyuki Ogata, a Tara Project collaborator and microbiologist at the Mediterranean Institute of Microbiology in Marseille, France, and his team dug through Tara Oceans data and found that a family of giant viruses called Megaviridae occurred alongside filamentous organisms known as oomycetes 5 . Evidence of gene transfer between the two organisms gives the first hints, say the researchers, that oomycetes might be hosts for giant viruses.…”